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TYW1 Gene(Protein Coding)

TRNA-YW Synthesizing Protein 1 Homolog

GCID:
GC07P066995
GIFtS:
53
Genes Participants
UDN Logo

Aliases for TYW1 Gene

Aliases for TYW1 Gene

  • TRNA-YW Synthesizing Protein 1 Homolog 2 3 5
  • Radical S-Adenosyl Methionine And Flavodoxin Domain-Containing Protein 1 3 4
  • Radical S-Adenosyl Methionine And Flavodoxin Domains 1 2 3
  • TRNA Wybutosine-Synthesizing Protein 1 Homolog 3 4
  • RSAFD1 3 4
  • S-Adenosyl-L-Methionine-Dependent TRNA 4-Demethylwyosine Synthase 3
  • TRNA-YW Synthesizing Protein 1 Homolog A (S. Cerevisiae) 2
  • TRNA-YW Synthesizing Protein 1 Homolog (S. Cerevisiae) 2
  • TRNA-YW Synthesizing Protein 1 Homolog A 3
  • TRNA-YW-Synthesizing Protein 4
  • EC 4.1.3.44 4
  • YPL207W 3
  • TYW1A 3

External Ids for TYW1 Gene

Previous HGNC Symbols for TYW1 Gene

  • RSAFD1

Previous GeneCards Identifiers for TYW1 Gene

  • GC07P066099
  • GC07P066460
  • GC07P062645

Summaries for TYW1 Gene

Entrez Gene Summary for TYW1 Gene

  • Wybutosine (yW) is a hypermodified guanosine found in phenylalanine tRNA adjacent to the anticodon that stabilizes codon-anticodon interactions in the ribosome. In yeast, the homolog of this gene is essential for the synthesis of wybutosine. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

GeneCards Summary for TYW1 Gene

TYW1 (TRNA-YW Synthesizing Protein 1 Homolog) is a Protein Coding gene. Among its related pathways are Gene Expression and tRNA processing. GO annotations related to this gene include oxidoreductase activity and 4 iron, 4 sulfur cluster binding. An important paralog of this gene is TYW1B.

UniProtKB/Swiss-Prot for TYW1 Gene

  • Probable component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in wybutosine biosynthesis (By similarity).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TYW1 Gene

Genomics for TYW1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for TYW1 Gene

Enhancers for TYW1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07G067127 1.9 FANTOM5 Ensembl ENCODE dbSUPER 36.5 +134.3 134261 3.3 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF766 FOS TYW1 RABGEF1 STAG3L4 LOC644794 MIR4650-1 GC07P067259
GH07G067162 1.1 ENCODE 53.7 +168.3 168338 1.2 HDGF PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 YY1 ZNF207 KLF13 ZNF263 TYW1 STAG3L4 LOC100420547 SPDYE21P ENSG00000229180 ENSG00000232546 ENSG00000244657 ENSG00000230189 MIR4650-1 GC07P067259
GH07G067102 1.3 Ensembl ENCODE dbSUPER 37.2 +109.5 109542 3.5 HDAC1 PKNOX1 ESRRA ARNT TAL1 ETV1 NCOR1 NFE2 HES1 SMARCE1 TYW1 STAG3L4 RABGEF1 MIR4650-1 ENSG00000233383
GH07G067099 1.1 ENCODE dbSUPER 37.3 +105.7 105703 1.9 HDAC1 CBX3 ARNT FEZF1 TCF12 EGR1 ZSCAN5C ZNF263 ZBTB2 ZEB2 TYW1 MIR4650-1 ENSG00000233383
GH07G066993 1.4 ENCODE dbSUPER 28.1 +0.5 523 4.3 HDGF FOXA2 PKNOX1 CREB3L1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 TYW1 ENSG00000229180 RABGEF1 ENSG00000244657 LOC100420547 ENSG00000232546 STAG3L4 ENSG00000230189 GTF2IP23 PMS2P4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TYW1 on UCSC Golden Path with GeneCards custom track

Promoters for TYW1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000213037 927 3801 HDGF FOXA2 PKNOX1 CREB3L1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2

Transcription factor binding sites by QIAGEN in the TYW1 gene promoter:

Genomic Location for TYW1 Gene

Chromosome:
7
Start:
66,995,173 bp from pter
End:
67,239,520 bp from pter
Size:
244,348 bases
Orientation:
Plus strand

Genomic View for TYW1 Gene

Genes around TYW1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TYW1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TYW1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TYW1 Gene

Proteins for TYW1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TYW1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NV66-TYW1_HUMAN
    Recommended name:
    S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase
    Protein Accession:
    Q9NV66
    Secondary Accessions:
    • Q6PJG8
    • Q75MG8
    • Q75MN3
    • Q86V12
    • Q8IVS7
    • Q9H9C4

    Protein attributes for TYW1 Gene

    Size:
    732 amino acids
    Molecular mass:
    83702 Da
    Cofactor:
    Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH15591.1; Type=Frameshift; Positions=663; Evidence={ECO:0000305}; Sequence=BAB14307.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for TYW1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TYW1 Gene

Protein Expression for TYW1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TYW1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TYW1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for TYW1 Gene

Domains & Families for TYW1 Gene

Protein Domains for TYW1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TYW1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NV66

UniProtKB/Swiss-Prot:

TYW1_HUMAN :
  • Belongs to the TYW1 family.
Family:
  • Belongs to the TYW1 family.
genes like me logo Genes that share domains with TYW1: view

No data available for Gene Families for TYW1 Gene

Function for TYW1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for TYW1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
N(1)-methylguanine(37) in tRNA(Phe) + pyruvate + S-adenosyl-L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + L-methionine + 5-deoxyadenosine + CO(2) + H(2)O.
UniProtKB/Swiss-Prot Function:
Probable component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in wybutosine biosynthesis (By similarity).

Enzyme Numbers (IUBMB) for TYW1 Gene

Gene Ontology (GO) - Molecular Function for TYW1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0010181 FMN binding IEA --
GO:0016829 lyase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0051536 iron-sulfur cluster binding IEA --
genes like me logo Genes that share ontologies with TYW1: view
genes like me logo Genes that share phenotypes with TYW1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for TYW1

CRISPR Products

miRNA for TYW1 Gene

miRTarBase miRNAs that target TYW1

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TYW1 Gene

Localization for TYW1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TYW1 gene
Compartment Confidence
nucleus 3
cytosol 3
plasma membrane 1
extracellular 1
peroxisome 1
endoplasmic reticulum 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for TYW1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TYW1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TYW1 Gene

Pathways & Interactions for TYW1 Gene

genes like me logo Genes that share pathways with TYW1: view

UniProtKB/Swiss-Prot Q9NV66-TYW1_HUMAN

  • Pathway: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.

Gene Ontology (GO) - Biological Process for TYW1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008033 tRNA processing IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with TYW1: view

No data available for SIGNOR curated interactions for TYW1 Gene

Drugs & Compounds for TYW1 Gene

Products:

  1. Drug

(2) Drugs for TYW1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
Flavin Mononucleotide Experimental Pharma 6
genes like me logo Genes that share compounds with TYW1: view

Transcripts for TYW1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TYW1 Gene

(3) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(167) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TYW1 Gene

TRNA-yW synthesizing protein 1 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TYW1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b
SP1:
SP2:
SP3:
SP4: -

Relevant External Links for TYW1 Gene

GeneLoc Exon Structure for
TYW1
ECgene alternative splicing isoforms for
TYW1

Expression for TYW1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TYW1 Gene

mRNA expression in normal human tissues for TYW1 Gene
mRNA expression by BioGPS for TYW1 GenemRNA expression by GTEx for TYW1 Gene

Protein differential expression in normal tissues from HIPED for TYW1 Gene

This gene is overexpressed in Spleen (65.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TYW1 Gene



Protein tissue co-expression partners for TYW1 Gene

NURSA nuclear receptor signaling pathways regulating expression of TYW1 Gene:

TYW1

SOURCE GeneReport for Unigene cluster for TYW1 Gene:

Hs.520917

Evidence on tissue expression from TISSUES for TYW1 Gene

  • Intestine(4.2)
  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with TYW1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TYW1 Gene

Orthologs for TYW1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TYW1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia TYW1 34
  • 98.94 (n)
-- 35
  • 96 (a)
 OneToMany
dog
(Canis familiaris)
 Mammalia -- 35
  • 88 (a)
 OneToMany
TYW1 34
  • 87.02 (n)
cow
(Bos Taurus)
 Mammalia TYW1 34 35
  • 86.59 (n)
mouse
(Mus musculus)
 Mammalia Tyw1 34 16 35
  • 80.75 (n)
rat
(Rattus norvegicus)
 Mammalia Tyw1 34
  • 80.39 (n)
oppossum
(Monodelphis domestica)
 Mammalia -- 35
  • 74 (a)
 OneToMany
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 35
  • 68 (a)
 OneToMany
chicken
(Gallus gallus)
 Aves TYW1 34
  • 76.65 (n)
-- 35
  • 70 (a)
 OneToMany
tropical clawed frog
(Silurana tropicalis)
 Amphibia tyw1 34
  • 69.43 (n)
Str.7207 34
zebrafish
(Danio rerio)
 Actinopterygii tyw1 34 35
  • 68.26 (n)
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_AFL099W 34
  • 52.57 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes TYW1 34 35 37
  • 50.53 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT1G75200 34
  • 56.09 (n)
soybean
(Glycine max)
 eudicotyledons Gma.17994 34
rice
(Oryza sativa)
 Liliopsida Os03g0775300 34
  • 56.72 (n)
Os.33461 34
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.8783 35
  • 57 (a)
 OneToMany
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPCC1020.08 34
  • 55.49 (n)
bread mold
(Neurospora crassa)
 Ascomycetes NCU06633 34
  • 50.48 (n)
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.5664 34
Species where no ortholog for TYW1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TYW1 Gene

ENSEMBL:
Gene Tree for TYW1 (if available)
TreeFam:
Gene Tree for TYW1 (if available)

Paralogs for TYW1 Gene

Paralogs for TYW1 Gene

(1) SIMAP similar genes for TYW1 Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for TYW1 Gene

genes like me logo Genes that share paralogs with TYW1: view

Variants for TYW1 Gene

Sequence variations from dbSNP and Humsavar for TYW1 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs113993990 Pathogenic 66,995,299(-) CTGGC(-/G)GAGCG upstream-variant-2KB, reference, frameshift-variant
rs28942099 Pathogenic 66,995,394(-) ACCAA(A/C)CAGAT upstream-variant-2KB, reference, missense
rs373730800 Pathogenic 66,995,320(+) TGTTT(C/G/T)TGTAG upstream-variant-2KB, reference, missense
rs886039431 Pathogenic 66,995,298(-) TGGCG(-/G)AGCGG upstream-variant-2KB, reference, frameshift-variant
rs1000013008 -- 67,171,130(+) TTTAC(A/G/T)TATTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TYW1 Gene

Variant ID Type Subtype PubMed ID
dgv11434n54 CNV loss 21841781
dgv11435n54 CNV loss 21841781
dgv1299e214 CNV gain 21293372
dgv1300e214 CNV gain 21293372
dgv3579n106 CNV deletion 24896259
esv2253832 CNV deletion 18987734
esv23402 CNV loss 19812545
esv2422035 CNV deletion 20811451
esv2467105 CNV deletion 19546169
esv26455 CNV loss 19812545
esv2660507 CNV deletion 23128226
esv2666250 CNV deletion 23128226
esv2759535 CNV gain 17122850
esv33653 CNV loss 17666407
esv3541815 CNV deletion 23714750
esv3571892 CNV loss 25503493
esv3571893 CNV loss 25503493
esv3571894 CNV loss 25503493
esv3571895 CNV loss 25503493
esv3571896 CNV loss 25503493
esv3613538 CNV loss 21293372
esv3613541 CNV loss 21293372
esv3613543 CNV loss 21293372
esv3891136 CNV gain 25118596
esv3891138 CNV gain 25118596
nsv1032237 CNV loss 25217958
nsv1032575 CNV gain 25217958
nsv1109885 CNV deletion 24896259
nsv1109886 CNV deletion 24896259
nsv1119126 CNV deletion 24896259
nsv1140797 CNV deletion 24896259
nsv1142671 CNV deletion 24896259
nsv1146102 OTHER inversion 26484159
nsv1161553 OTHER complex 26073780
nsv441983 CNV loss 18776908
nsv509205 CNV insertion 20534489
nsv5774 CNV insertion 18451855
nsv607415 CNV loss 21841781
nsv607418 CNV loss 21841781
nsv607423 CNV loss 21841781
nsv824151 CNV loss 20364138
nsv831019 CNV loss 17160897
nsv966838 CNV duplication 23825009
nsv970518 CNV duplication 23825009
nsv981515 CNV duplication 23825009
nsv981516 CNV duplication 23825009

Variation tolerance for TYW1 Gene

Residual Variation Intolerance Score: 76.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.17; 90.39% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TYW1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TYW1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TYW1 Gene

Disorders for TYW1 Gene

Relevant External Links for TYW1

Genetic Association Database (GAD)
TYW1
Human Genome Epidemiology (HuGE) Navigator
TYW1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TYW1

No disorders were found for TYW1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TYW1 Gene

Publications for TYW1 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  2. Ribonucleome analysis identified enzyme genes responsible for wybutosine synthesis. (PMID: 17150819) Noma A. … Suzuki T. (Nucleic Acids Symp Ser (Oxf) 2006) 2 3 64
  3. Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. (PMID: 16162496) Waas W.F. … Schimmel P. (J. Biol. Chem. 2005) 2 3 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for TYW1 Gene

Sources for TYW1 Gene

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